application: prettyplot [
  documentation: "Draw a sequence alignment with pretty formatting"
  groups: "Alignment:Multiple, Display"
  relations: "EDAM:0000182 topic Sequence alignment"
  relations: "EDAM:0000092 topic Data rendering and visualisation"
  relations: "EDAM:0000562 operation Sequence alignment reformatting"
  relations: "EDAM:0000564 operation Sequence rendering"
]

section: input [
  information: "Input section"
  type: "page"
]

  seqset: sequences [
    parameter: "Y"
    type: "gapany"
    aligned: "Y"
    relations: "EDAM:0000863 data Sequence alignment"
  ]

  matrix: matrixfile [
    additional: "Y"
    information: "Matrix file"
    protein: "$(acdprotein)"
    help: "This is the scoring matrix file used when comparing
           sequences. By default it is the file 'EBLOSUM62' (for proteins) or
           the file 'EDNAFULL' (for nucleic sequences). These files are
           found in the 'data' directory of the EMBOSS installation."
    relations: "EDAM:0000874 data Comparison matrix"
  ]

endsection: input

section: additional [
  information: "Additional section"
  type: "page"
]

  integer: residuesperline [
    additional: "Y"
    default: "50"
    information: "Number of residues to be displayed on each
                  line"
    help: "The number of residues to be displayed on each line"
    relations: "EDAM:0001249 data Sequence length"
  ]

  integer: resbreak [
    additional: "Y"
    minimum: "1"
    maximum: "$(residuesperline)"
    failrange: "N"
    trueminimum: "Y"
    information: "Residues before a space"
    default: "$(residuesperline)"
    expected: "Same as -residuesperline to give no breaks"
    relations: "EDAM:0001249 data Sequence length"
  ]

  boolean: ccolours [
    additional: "Y"
    default: "Y"
    information: "Colour residues by their consensus value."
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  string: cidentity [
    additional: "Y"
    information: "Colour to display identical residues (RED)"
    default: "RED"
    knowntype: "plot colour"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  string: csimilarity [
    additional: "Y"
    information: "Colour to display similar residues (GREEN)"
    default: "GREEN"
    knowntype: "plot colour"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  string: cother [
    additional: "Y"
    information: "Colour to display other residues (BLACK)"
    default: "BLACK"
    knowntype: "plot colour"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: docolour [
    additional: "Y"
    information: "Colour residues by table oily, amide etc."
    default: "N"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  string: shade [
    additional: "Y"
    information: "Shading"
    help: "Set to BPLW for normal shading \
           (black, pale, light, white) \
           so for pair = 1.5,1.0,0.5 and shade = BPLW \
           Residues score Colour \
           1.5 or over... BLACK (B) \
           1.0 to 1.5 ... BROWN (P) \
           0.5 to 1.0 ... WHEAT (L) \
           under 0.5 .... WHITE (W) \
           The only four letters allowed are BPLW, in any order."
    default: ""
    maxlength: "4"
    minlength: "0"
    knowntype: "plot shading"
    pattern: "^([BPLW]{4})?$"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  array: pair [
    additional: "Y"
    information: "Values to represent identical similar
                  related"
    default: "1.5,1.0,0.5"
    minimum: "0.0"
    size: "3"
    sumtest: "N"
    knowntype: "threshold identity similar related"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  integer: identity [
    additional: "Y"
    information: "Only match those which are identical in all
                  sequences."
    default: "0"
    minimum: "0"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: box [
    additional: "Y"
    information: "Display prettyboxes"
    default: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: boxcol [
    additional: "Y"
    information: "Colour the background in the boxes"
    default: "N"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  string: boxuse [
    additional: "Y"
    information: "Colour to be used for background. (GREY)"
    default: "GREY"
    knowntype: "plot colour"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: name [
    additional: "Y"
    information: "Display the sequence names"
    default: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  integer: maxnamelen [
    additional: "Y"
    information: "Margin size for the sequence name."
    default: "10"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: number [
    additional: "Y"
    information: "Display the residue number"
    default: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  boolean: listoptions [
    additional: "Y"
    information: "Display the date and options used"
    default: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  float: plurality [
    additional: "Y"
    information: "Plurality check value (totweight/2)"
    default: "@( $(sequences.totweight) / 2)"
    expected: "Half the total sequence weighting"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

  section: consensussection [
    information: "Consensus section"
    type: "frame"
  ]

    boolean: consensus [
      additional: "Y"
      information: "Display the consensus"
      default: "N"
    relations: "EDAM:0002527 data Parameter or primitive"
    ]

    boolean: collision [
      additional: "Y"
      information: "Allow collisions in calculating consensus"
      default: "Y"
    relations: "EDAM:0002527 data Parameter or primitive"
    ]

    list: alternative [
      additional: "Y"
      information: "Use alternative collisions routine"
      values: "0:Normal collision check. (default); 1:Compares
               identical scores with the max score found. So if any other
               residue matches the identical score then a collision has
               occurred.; 2:If another residue has a greater than or equal to
               matching score and these do not match then a collision has
               occurred.; 3:Checks all those not in the current consensus.If
               any of these give a top score for matching or identical scores
               then a collision has occured."
      help: "Values are 0:Normal collision check. (default) \
             1:Compares identical scores with the max score found. So if any
             other residue matches the identical score then a collision has
             occurred. \
             2:If another residue has a greater than or equal to matching
             score and these do not match then a collision has occurred. \
             3:Checks all those not in the current consensus.If any of these
             give a top score for matching or identical scores then a
             collision has occured."
      default: "0"
      minimum: "1"
      maximum: "1"
    relations: "EDAM:0002527 data Parameter or primitive"
    ]

  endsection: consensussection

  integer: showscore [
    additional: "Y"
    information: "Print residue scores"
    default: "-1"
    relations: "EDAM:0002152 data Rendering parameter"
  ]

  boolean: portrait [
    additional: "Y"
    information: "Set page to Portrait"
    default: "N"
    relations: "EDAM:0002527 data Parameter or primitive"
  ]

endsection: additional

section: output [
  information: "Output section"
  type: "page"
]

  graph: graph [
    standard: "Y"
    gdesc: "Pretty plot"
    relations: "EDAM:0001711 data Sequence alignment image or plot"
  ]

endsection: output